In North Park last month, days before his political life was turned upside down by a spate of sexual harassment allegations, Mayor Bob Filner appeared outside a half-demolished Jack in the Box to decry the company’s renovation plan.

The construction, already permitted by the city, ground to a halt.

U-T Watchdog reported last month that the FBI is investigating Filner’s role in two major developments that were stopped and restarted after project officials agreed to six-figure concessions.

But San Diego’s second strong mayor has inserted himself into numerous projects besides those developments, known as Sunroad Centrum Partners in Kearny Mesa and Centrepoint apartments in the College Area.

“We’ve heard chatter within our industry that investors are getting a little leery of coming to San Diego with all of the uncertainty that is in play right now,” said Matt Adams, vice president of the Building Industry Association of San Diego County.

Adams said the uncertainty he referred to had nothing to do with the sexual harassment claims and subsequent calls for Filner’s resignation.

“The classic examples you’ve seen certainly contradict the mayor’s statements when he was inaugurated and in his State of the City address, where he pledged to promote regulatory certainty,” he said.

The Mayor’s Office did not respond to requests to discuss Filner’s decisions to intervene in development projects since he was sworn in last December.

Earlier this year, Filner intervened at a community planning meeting to oppose a 23-acre project in Carmel Valley, saying the 2.1 million square foot mixed-use project was far bigger than what the neighborhood wanted. Los Angeles developer Kilroy Realty subsequently downsized the One Paseo residential-retail-office complex by one-third and is awaiting approval from City Hall.

Filner's office intervened in proposal to tear down and replace this 1925 cottage in La Jolla.

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Filner's office intervened in proposal to tear down and replace this 1925 cottage in La Jolla.

Even a tiny lot in La Jolla, where husband-and-wife investors sought to tear down their 1925 cottage to make way for a gleaming duplex, has not escaped the mayor’s notice. In June, Filner pulled that application from a planning-board agenda and sent it to the city’s Historic Resources Board even though staff had previously said the home was not historically significant.

“Right now, the only certainty is if you start to develop a project, you don’t know if it’s going to be stopped, even if you’ve got all of the permits and it’s coming out of the ground,” former Mayor Jerry Sanders said this past week in calling for Filner’s resignation.

He also said, “When you’re seeing the Sunroad fiasco and the Centrepoint fiasco, what you see is businesses not willing to invest if there’s not certainty.”

Supporters point out that much of Filner’s campaign centered on his plans to improve San Diego neighborhoods rather than direct the power of the Mayor’s Office downtown or to service the development community.

“The mayor is doing what should have been done for a long time,” said Bruce Coons of Save Our Heritage Organisation, a nonprofit preservation group. “If a project is not done according to code or zoning or plan, there should be some overriding benefit to the community.”

Sunroad cut two checks to City Hall totaling $100,000 after Filner vetoed revisions to a residential complex the firm is building in Kearny Mesa. The money was aimed at a veterans memorial and a bike event favored by the mayor.

Filner returned the money in late June, on the same day the Watchdog reported that a voice-mail message to City Hall established a link between the donations and the mayor’s decision to reverse himself and approve the changes.

Federal law makes it illegal for public officials to accept money in exchange for performing specific acts. The mayor denied changing his mind on the Sunroad project due to the donation, but a former top deputy told the Watchdog that is exactly what happened.

FBI agents opened an investigation into the transaction within days.

Last week, the Watchdog reported that federal agents expanded their probe to include Centrepoint, a 332-unit apartment complex in the College Area whose owners paid $150,000 to lift an “administrative hold” Filner placed on that development.

FBI agents have interviewed one lawyer at the firm representing developer Carmel Partners and requested an interview with a second. Officials at City Hall also have been asked about Centrepoint.

As to the Jack in the Box project, spokesman Brian Luscomb said renovations at the North Park restaurant restarted last week after the company and city officials reached an unspecified agreement.

“There were no concessions” paid by Jack in the Box, he said.

For the Carmel Valley project, Los Angeles attorney Benjamin Reznik declined to discuss the mayor’s decision to intervene in January or the subsequent downsizing of the project to 1.4 million square feet.

Regarding the La Jolla cottage on Playa Del Sur, Karen Visin approached the Watchdog with a complaint that Filner wrongly derailed her plan to demolish an aging cottage and replace it with a two-unit dwelling.

“Now we must face another 2 months of delay even though every single time staff has reviewed the facts they have thoroughly rebuked any notion that our property is historic,” she wrote.

Visin has now hired a lawyer to negotiate a resolution with City Hall.

Sanders, the chamber director who termed out as San Diego mayor in December, was widely considered a more business-friendly chief executive than his successor.

Under his watch, for example, the city adopted a program that allowed developers to defer impact fees until their buildings received occupancy certificates.

“That’s gone. That’s one of the first things (Filner) did is inform us he wasn’t going to sign fee deferrals any more,” said Adams, the building industry executive. “When you’re looking at a market in recovery with very tight margins, that could make the difference as to whether a project will pencil (out).”

Joshua Chanin, a professor in the School of Public Affairs at San Diego State University, said decisions like that are what voters expected when they approved the chief-executive form of government in 2010.

“This is what you get under the strong-mayor system,” he said. “His office is in charge of the bureaucracy. The permitting process falls under his purview.

“The mayor’s specific involvement in decisions that have already been made by bureaucrats does seem to inject a certain amount of politics into these decisions,” Chanin said. “But proponents of the strong-mayor system suggested this is the way it should work.”